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3. GS Amplicon Variant Analyzer Command Line Interface : 3.2 AVA-CLI Command Language Overview : 3.2.2 Available Commands
3.2.2
Available Commands
The top level commands recognized by the AVA-CLI are introduced briefly below. Some of the commands like “set” don’t act directly on any entity type, while many others can be used to act on more than one entity type. The full set of online help showing the usage statements for the many ways these commands can be used may be found in section 3.4.
In general, you can create the Project and the objects within it using the “create” command (except the Read Data Sets, which must be added to the Project via a specialized “load” command). Many of the commands accept input in a tabular format that enables bulk import and allows you to process many objects at a time rather than forcing you to fully specify a command for each individual object. Once you have objects in the Project, they can be edited using the “update” and “rename” commands or they can be deleted from the Project entirely with the “remove” command. Associations between Read Data Sets, Samples, and Amplicons can be managed via the “associate” and “dissociate” commands. Computation can be automatically triggered and managed via the “computation” family of commands. Certain “utility” commands can be used to validate the Project and to export data. There are also several other commands (such as “set”, “save”, “close”, and “exit”) used to control interaction with the CLI and for other miscellaneous functions.
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associate – This command makes associations between appropriate records. It may be abbreviated to “assoc”. It accepts tabular input. A full usage statement is available in section 3.4.1.
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close – This command closes the Project that is currently open. A full usage statement is available in section 3.4.2.
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computation – The command controls computations on the Project. It may be abbreviated to “comp”. A full usage statement is available in section 3.4.3.
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create – This command creates entities including Projects, Reference Sequences, Amplicons, Samples, Variants, MIDs / MID Groups, Multiplexers, and Read Groups. It accepts tabular input. A full usage statement is available in section 3.4.4.
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dissociate – This command removes associations between records. It may be abbreviated to “dissoc”. It accepts tabular input. A full usage statement is available in section 3.4.5.
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exit – This command exits the interpreter. A full usage statement is available in section 3.4.6.
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list – This command lists information about entities. It can optionally send output to a file. A full usage statement is available in section 3.4.7.
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load – This command loads Read Data Sets into the Project that is currently open. It accepts tabular input. A full usage statement is available in section 3.4.8.
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open – This command loads a pre-existing Project, making it the current open Project in the CLI. A full usage statement is available in section 3.4.9.
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remove – This command removes records from a Project. It accepts tabular input. A full usage statement is available in section 3.4.10.
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rename – This command renames entities. It accepts tabular input. A full usage statement is available in section 3.4.11.
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report – This command produces reports about computations including Variant frequencies and alignments, in multiple formats. A full usage statement is available in section 3.4.12.
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save – This command saves any modifications to the Project that is currently open. A full usage statement is available in section 3.4.13.
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set – This command sets environment variables. A full usage statement is available in section 3.4.14.
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show – This command is used to show various information about the interpreter. A full usage statement is available in section 3.4.15.
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update – This command updates entities' properties. It accepts tabular input. A full usage statement is available in section 3.4.16.
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utility - This command performs utility functions such as Project cloning. A full usage statement is available in section 3.4.17.